FORT MEADE, Md. — Defense Secretary Lloyd Austin'’ surprise decision to throw out a plea deal with accused 9/11 mastermind Khalid Sheikh Mohammed and two of his co-defendants has left their case at Guantanamo Bay, Cuba, in disarray, with the defense, prosecution and judge all uncertain about when and how it would move forward.

A court session on Wednesday was the first since the Pentagon released notice of Austin's decision late Friday. The plea agreement, which would have spared the defendants the risk of the death penalty, generated strong feelings among both opponents and supporters of the deal, including the families of Sept. 11 victims. It drew intense criticism of the Biden administration from senior Republican lawmakers.

The disruption caused by the unexpected override of the plea deal was just the latest to hit the special U.S. military-run commissions and their more than decadelong effort to bring the men accused of killing nearly 3,000 people on Sept. 11, 2001, to trial.

The unusual location and nature of the offshore commissions, and legal challenges, including those stemming from the torture the men underwent in CIA custody in the first years after their capture, all have contributed to the delays, keeping the case still in pre-trial hearings.

Defense attorneys on Wednesday said they would challenge the legality of Austin's order and suspended their participation in hearings until those challenges were resolved. They contended that the plea deal still stood.

Walter Ruiz, an attorney for 9/11 defendant Mustafa al Hawsawi, said Austin’s order suggested “unlawful interference at the highest levels of government.”

More broadly, Ruiz said, it raised questions “whether we can ethically continue to engage” in the Pentagon-run military commission in the face of an action “that goes right at the heart of the integrity of the system itself.”

Military prosecutors also appeared taken by surprise by Austin's intervention. Lead prosecutor Clay Trivett raised the prospect of having to freeze other litigation in the case as they try to learn what led to his decision and work through the legal issues it raises.

“We do not have our position fully articulated and coordinated throughout the U.S. government on this,” Trivett told the court. “It shouldn't be expected only a couple of days after the fact.”

The 9/11 attacks were among the most damaging and deadly on the U.S. in its history. In the al-Qaida plot, hijackers commandeered four passenger airliners and flew them into the World Trade Center and the Pentagon, with the fourth coming down in a field in Pennsylvania.

Former President George W. Bush and his Defense Secretary Donald Rumsfeld set up the initial military commissions for the 9/11 defendants and other foreigners as the U.S. pursued what it called its war on terror.

The new developments unfolded after the Pentagon-approved chief authority over the military commission, Susan Escallier, approved the plea agreement between the military-appointed prosecutors and defense attorneys. The deal had been two years in the making.

Austin said in Friday’s order that he was overriding Escallier’s approval and taking direct control of such decisions in the 9/11 case going forward.

On Tuesday, he cited the American losses and sacrifice in the 2001 attacks and the subsequent U.S. military offensives against al-Qaida and other extremist groups.

“I have long believed that the families of the victims, our service members, and the American public deserve the opportunity to see military commissions, commission trials carried out,” he told reporters.

A senior defense official, speaking to reporters on condition of anonymity to discuss administration thinking, said news of the plea deal came as a surprise to Austin and other officials, despite the long and publicly reported negotiations that led to it.

Asked whether political pressure and election-year considerations influenced the reversal, the official said, “That had nothing to do with the decision that the secretary made.”

White House press secretary Karine Jean-Pierre said the decision was Austin’s. “We had nothing to do with the 9/11 plea deal reversal,” she said.

On Wednesday, the judge overseeing the case, Air Force Col. Matthew McCall, vowed not to be influenced by any additional outside pressure.

“If more political pressure is put on the parties to make a decision one way or the other,” that could build the case for illegal interference in the case, “but … it’s not going to affect me,” McCall told prosecutors, defense attorneys and defendants, including Mohammed, who listened intently and spoke with his lawyers. Reporters were able to monitor the proceedings from Fort Meade, Maryland.

McCall agreed to excuse the defense attorneys from participating in the pre-trial hearings while expected challenges to Austin's actions play out.

Gary Sowards, the lead attorney for Mohammed, the accused mastermind of the 9/11 attacks, warned the court on Wednesday that that process alone was likely to take up to two years.

“To intervene in this most unusual way ensures total chaos from this point forward,” Sowards told McCall, referring to Austin's action.

Under the plea agreement, Mohammed, Hawsawi, and fellow defendant Walid bin Attash would have entered guilty pleas in exchange for the government not seeking the death penalty against them.

Defense attorneys stressed Wednesday the agreement would have committed the accused to answer any lingering questions about the attack from family members of victims and others.

After Wednesday's tumultuous start, the hearing proceeded with the questioning of an FBI witness, with the active defense participation of only one defendant who had not taken the plea agreement, Aamar al Baluchi.